Search results for " Typing"
showing 10 items of 273 documents
Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"
2011
International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …
Phylogenetic analysis of environmental Legionella pneumophila isolates from an endemic area (Alcoy, Spain).
2015
Environmental surveillance of Legionella pneumophila is a key component of the control measures established in urban settlements to ensure water safety and quality, with the aim of minimizing and limiting opportunistic infections in humans. In this work, we present results on the detection and genetic characterization of these bacteria in the outbreak-recurrent region of Alcoy (Comunidad Valenciana, Spain) using water and biofilm samples. We were particularly interested in studying the presence and distribution of L. pneumophila in the absence of outbreak or sporadic cases of legionellosis and in comparing the efficacy of culturing from water samples with a biofilm-based detection procedure…
Snapshot of Moving and Expanding Clones of Mycobacterium tuberculosis and Their Global Distribution Assessed by Spoligotyping in an International Stu…
2003
ABSTRACT The present update on the global distribution of Mycobacterium tuberculosis complex spoligotypes provides both the octal and binary descriptions of the spoligotypes for M. tuberculosis complex, including Mycobacterium bovis , from >90 countries (13,008 patterns grouped into 813 shared types containing 11,708 isolates and 1,300 orphan patterns). A number of potential indices were developed to summarize the information on the biogeographical specificity of a given shared type, as well as its geographical spreading (matching code and spreading index, respectively). To facilitate the analysis of hundreds of spoligotypes each made up of a binary succession of 43 bits of information, …
Prevalence and genotypes of Borrelia burgdorferi sensu lato infection in Ixodes ricinus ticks in southern Norway.
2010
From April to October 2007, host-seeking Ixodes ricinus ticks were collected from 4 locations in southern Norway: Farsund, Mandal, Sogne and Tromoy. Two hundred and ten larvae, 1130 nymphs and 449 adults were investigated for infection with Borrelia burgdorferi sensu lato (s.l.) by real-time polymerase chain reaction (PCR) amplification of the 16S rRNA gene. The total percentage of B. burgdorferi s.l. in nymphal and adult ticks was determined to be 31.3% in Farsund, 25.2% in Mandal, 22.3% in Sogne and 22.1% in Tromoy. Larvae were pooled in groups of 10 before analysis, and Borrelia infection was detected in 1 of the 21 larvae pools. B. burgdorferi s.l. were genotyped by melting curve analys…
Development of a modified DNA extraction method for pulsed-field gel electrophoresis analysis of Staphylococcus aureus and enterococci without using …
2010
A modified pulsed-field gel electrophoresis (PFGE) protocol was developed and applied to clinical isolates of Staphylococcus aureus and enterococci to reduce the cost of using lysostaphin. This protocol reduces the expenses of PFGE typing of S. aureus and enterococci as it removes the use of lysostaphin during the spheroplast formation from these bacteria.
Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods
2013
Identifiant HAL : hal-01120618; International audience; Soil is a potential reservoir of human pathogens and a possible source of contamination of animals, crops and water. In order to study the distribution of Listeria monocytogenes in French soils, a real-time PCR TaqMan assay targeting the phosphoribosylpyrophosphate synthetase (prs) gene of L. monocytogenes was developed for the specific detection and quantification of this bacterium within a collection of 1315 soil DNAs originated from the French Soil Quality Monitoring Network. The prs real-time PCR TaqMan assay was specific for L. monocytogenes and could quantify accurately down to 104L. monocytogenes per gram of dry soil. Among the …
Global Distribution of Shigella sonnei Clones
2011
To investigate global epidemiology of Shigella sonnei, we performed multilocus variable number tandem repeat analysis of 1,672 isolates obtained since 1943 from 50 countries on 5 continents and the Pacific region. Three major clonal groups were identified; 2 were globally spread. Type 18 and its derivatives have circulated worldwide in recent decades.
Comparative evaluation of three different genotyping methods for investigation of nosocomial outbreaks of Legionnaires' disease in hospitals.
2000
ABSTRACT The increased incidence of nosocomial Legionnaires' disease in two hospitals prompted investigation of possible environmental sources. In the search for an effective DNA-typing technique for use in hospital epidemiology, the performance and convenience of three methods— Sfi I macrorestriction analysis (MRA), amplified fragment length polymorphism (AFLP), and arbitrarily primed PCR (AP-PCR)—were compared. Twenty-nine outbreak-associated and eight nonassociated strains of Legionella pneumophila with 13 MRA types and subtypes were investigated. These strains comprised isolates from bronchoalveolar lavages, from environmental, patient-related sources, and type strains. All three typing…
Helicobacter pylori: clonal population structure and restricted transmission within families revealed by molecular typing.
2000
ABSTRACT Helicobacter pylori infects up to 50% of the human population worldwide. The infection occurs predominantly in childhood and persists for decades or a lifetime. H. pylori is believed to be transmitted from person to person. However, tremendous genetic diversity has been reported for these bacteria. In order to gain insight into the epidemiological basis of this phenomenon, we performed molecular typing of H. pylori isolates from different families. Fifty-nine H. pylori isolates from 27 members of nine families were characterized by using restriction fragment length polymorphism analysis of five PCR-amplified genes, by pulsed-field gel electrophoresis (PFGE) of chromosomal DNA, and …
Relative reproductive success of co-infecting parasite genotypes under intensified within-host competition.
2015
In nature, host individuals are commonly simultaneously infected with more than one genotype of the same parasite species. These co-infecting parasites often interact, which can affect their fitness and shape host-parasite ecology and evolution. Many of such interactions take place through competition for limited host resources. Therefore, variation in ecological factors modifying the host resource level could be important in determining the intensity of competition and the outcome of co-infections. We tested this hypothesis by measuring the relative reproductive success of co-infecting genotypes of the trematode parasite Diplostomum pseudospathaceum in its snail host Lymnaea stagnalis whil…